LAMMPS (10 Mar 2021)
  using 1 OpenMP thread(s) per MPI task
# sample surface deposition script for molecules

units		lj
atom_style      bond
boundary        p p f

lattice		fcc 1.0
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
region          box block 0 5 0 5 0 10
create_box      3 box bond/types 1 extra/bond/per/atom 1
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011)
  1 by 1 by 1 MPI processor grid

region		substrate block INF INF INF INF INF 3
create_atoms	1 region substrate
Created 350 atoms
  create_atoms CPU = 0.001 seconds

pair_style	lj/cut 2.5
pair_coeff	* * 1.0 1.0
pair_coeff	1 2 1.0 1.0 5.0
mass		* 1.0

bond_style	harmonic
bond_coeff      1 5.0 1.0

neigh_modify	delay 0

molecule        dimer molecule.dimer
Read molecule template dimer:
  1 molecules
  2 atoms with max type 3
  1 bonds with max type 1
  0 angles with max type 0
  0 dihedrals with max type 0
  0 impropers with max type 0
region          slab block 0 5 0 5 8 9

group		addatoms empty
0 atoms in group addatoms
region          mobile block 0 5 0 5 2 INF
group		mobile region mobile
150 atoms in group mobile

compute	add addatoms temp
compute_modify	add dynamic/dof yes extra/dof 0

fix		1 addatoms rigid/small molecule mol dimer
  create bodies CPU = 0.000 seconds
  0 rigid bodies with 0 atoms
  1.0000000 = max distance from body owner to body atom
fix		2 mobile langevin 0.1 0.1 0.1 587283
fix		3 mobile nve

fix		4 addatoms deposit 100 0 100 12345 region slab near 1.0                 mol dimer vz -1.0 -1.0 rigid 1
fix		5 addatoms wall/reflect zhi EDGE

thermo_style	custom step atoms temp epair etotal press
thermo          100
thermo_modify	temp add lost/bond ignore lost warn
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:468)

#dump		1 all atom 50 dump.deposit.atom

#dump		2 all image 50 image.*.jpg type type #		axes yes 0.8 0.02 view 80 -30
#dump_modify	2 pad 5

#dump		3 all movie 50 tmp.mpg type type #		axes yes 0.8 0.02 view 80 -30
#dump_modify	3 pad 5

run             10000
WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182)
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 5.3
  ghost atom cutoff = 5.3
  binsize = 2.65, bins = 3 3 6
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.929 | 5.929 | 5.929 Mbytes
Step Atoms Temp E_pair TotEng Press 
       0      350            0   -6.9215833   -6.9215833   -1.0052629 
     100      352    1.0079368   -6.8875167   -6.8803581  -0.73353914 
     200      354    1.0081552   -6.8594643   -6.8452248  -0.70421276 
     300      356    1.0085803   -6.8171524   -6.7959042   -0.6917826 
     400      358    1.0099188   -6.7852701   -6.7570601  -0.70371699 
     500      360    1.0140221   -6.7493429   -6.7141338  -0.68415307 
     600      362     1.026148   -6.7105231   -6.6680032  -0.68314418 
     700      364    1.0683344   -6.6725162    -6.621154  -0.65747369 
     800      366    1.0958952   -6.6412275   -6.5813425  -0.68789614 
     900      368    1.1250033   -6.6101882    -6.541404  -0.66674346 
    1000      370    1.2326373   -6.5993719   -6.5160856   -0.6968868 
    1100      372    1.1397426   -6.5912861   -6.5070309  -0.63330356 
    1200      374    1.0514292   -6.5905747   -6.5062354  -0.71020362 
    1300      376     1.003296   -6.5747765   -6.4880555  -0.65459732 
    1400      378   0.82999289   -6.5681797   -6.4913285  -0.60438126 
    1500      380   0.90239175    -6.575298   -6.4862461  -0.66528725 
    1600      382   0.86399799   -6.5692206   -6.4787496  -0.65027781 
    1700      384   0.64747231   -6.5644237   -6.4927634   -0.6304614 
    1800      386   0.74288971   -6.5515735   -6.4649672  -0.67772325 
    1900      388    0.7257202   -6.5565091   -6.4676644  -0.66173549 
    2000      390   0.73381036   -6.5631515   -6.4690733  -0.64685916 
    2100      392   0.76476562   -6.5574124   -6.4549885  -0.68866192 
    2200      394   0.65932468   -6.5511557    -6.459118  -0.71728829 
    2300      396   0.70269509   -6.5728146   -6.4707819  -0.64362081 
    2400      398   0.60528919   -6.5845991   -6.4933494  -0.63956327 
    2500      400   0.51025744   -6.5812452   -6.5015175  -0.68706961 
    2600      402    0.5245131   -6.6003894   -6.5155801  -0.68972215 
    2700      404   0.46330251   -6.5659175   -6.4885092  -0.72870942 
    2800      406   0.48039778   -6.5715192    -6.488692    -0.753758 
    2900      408   0.53698616   -6.5813154   -6.4858951  -0.67117541 
    3000      410   0.50231419   -6.5886963   -6.4968096  -0.71905351 
    3100      412   0.49420225    -6.596733   -6.5037702  -0.65947518 
    3200      414   0.42703699   -6.5879338   -6.5054146  -0.80033546 
    3300      416   0.44306009    -6.580249   -6.4923825  -0.76503083 
    3400      418   0.55620672   -6.5923388   -6.4792346  -0.69367877 
    3500      420   0.39815033   -6.5911154   -6.5081674  -0.65569211 
    3600      422   0.44197847   -6.6026382   -6.5083774  -0.73299102 
    3700      424   0.45049389   -6.6060616   -6.5077817   -0.7552914 
    3800      426   0.43047295   -6.6079275     -6.51193  -0.71501328 
    3900      428   0.43779129   -6.6099306   -6.5102001  -0.71539515 
    4000      430   0.41113503   -6.6123009   -6.5166881  -0.74177096 
    4100      432   0.32800011   -6.5983566   -6.5205325  -0.71688103 
    4200      434   0.39168203   -6.6110342   -6.5162724  -0.78927697 
    4300      436   0.48151013   -6.6183315   -6.4996106  -0.70523035 
    4400      438   0.45391027   -6.6331732   -6.5191775   -0.7270855 
    4500      440     0.349126   -6.6091657   -6.5199006  -0.76974115 
    4600      442   0.43375023   -6.6219188   -6.5090653  -0.74576212 
    4700      444   0.40071749   -6.6184164   -6.5123707  -0.71919052 
    4800      446     0.414292   -6.6298132   -6.5183445  -0.76237313 
    4900      448   0.44210681   -6.6364174   -6.5155288  -0.78753121 
    5000      450   0.36101771   -6.6232703   -6.5229876  -0.73927083 
    5100      452   0.41481171   -6.6442404   -6.5272305  -0.76316209 
    5200      454   0.40283527   -6.6512252   -6.5358759  -0.79645689 
    5300      456    0.3642061   -6.6530346   -6.5472072  -0.77458364 
    5400      458   0.38449826   -6.6514864   -6.5381518  -0.73083784 
    5500      460   0.42559408   -6.6769326   -6.5497169  -0.78932279 
    5600      462   0.38905756   -6.6698705   -6.5519743  -0.77118812 
    5700      464   0.38354955   -6.6706904   -6.5528977  -0.75067129 
    5800      466   0.36760943   -6.6942519   -6.5798669    -0.685487 
    5900      468   0.30783118   -6.6838159   -6.5867965  -0.79233808 
    6000      470   0.33145368   -6.6733504   -6.5675673  -0.84390449 
    6100      472   0.39252324   -6.6912189   -6.5643973  -0.83342022 
    6200      474   0.32342144   -6.6906083   -6.5848481  -0.71262158 
    6300      476   0.34445238   -6.7008453   -6.5868721  -0.76650756 
    6400      478   0.38152782   -6.7017838   -6.5740758  -0.77113022 
    6500      480   0.37540166   -6.7119996   -6.5849105  -0.79907635 
    6600      482    0.3579419   -6.7034721   -6.5809401   -0.8141269 
    6700      484   0.33538235   -6.6916682    -6.575601  -0.83265486 
    6800      486   0.34081871   -6.6931924    -6.573976  -0.80582583 
    6900      488    0.3555283   -6.6939997   -6.5683263  -0.74771423 
    7000      490    0.3543769   -6.7093364   -6.5827732  -0.77643516 
    7100      492   0.31263107    -6.698361   -6.5855723  -0.73108333 
    7200      494      0.32107   -6.6959056   -6.5789166   -0.7575478 
    7300      496   0.32908165   -6.7137605    -6.592677  -0.86538023 
    7400      498   0.32539571   -6.7030353   -6.5821554  -0.79337428 
    7500      500   0.33902577   -6.7078178   -6.5806832  -0.85408988 
    7600      502   0.35530921    -6.707507   -6.5730274  -0.79914613 
    7700      504   0.32391812   -6.6978823   -6.5741635  -0.78603595 
    7800      506   0.36390015   -6.7151325   -6.5748943  -0.83164222 
    7900      508    0.3372561   -6.7086718   -6.5775535   -0.7949992 
    8000      510   0.36612946   -6.7225238   -6.5789437  -0.80322866 
    8100      512   0.34622305   -6.7229825   -6.5860486  -0.70478659 
    8200      514    0.3212233   -6.7202524   -6.5921381  -0.91836713 
    8300      516    0.3402461    -6.721488   -6.5846642  -0.88273592 
    8400      518   0.34070258   -6.7268378   -6.5887152  -0.76057264 
    8500      520   0.36267747    -6.744602   -6.5963924  -0.81051317 
    8600      522    0.3439948   -6.7376267    -6.595943  -0.84600203 
    8700      524   0.30960289   -6.7276471   -6.5991382  -0.90965986 
    8800      526   0.28868972   -6.7159628    -6.595218    -0.876093 
    8900      528   0.31020216   -6.7162903   -6.5855707  -0.83193125 
    9000      530   0.31836275   -6.7171479   -6.5819939  -0.82093897 
    9100      532   0.32543293    -6.724167   -6.5850016   -0.7690143 
    9200      534   0.32644265   -6.7139575   -6.5733549  -0.86903096 
    9300      536   0.33050759   -6.7254715   -6.5821077  -0.94504522 
    9400      538   0.30372582   -6.7139931   -6.5813247  -0.91128612 
    9500      540   0.32943659   -6.7206223   -6.5757312  -0.87818439 
    9600      542   0.30911968    -6.708091   -6.5712114  -0.79092372 
    9700      544   0.33909826   -6.7222948   -6.5711342  -0.80266151 
    9800      546   0.29015141   -6.7086869   -6.5784908  -0.87763769 
    9900      548   0.33838474   -6.7384955   -6.5856667  -0.85630604 
   10000      550   0.30213198   -6.7338924   -6.5965597  -0.75738882 
Loop time of 17.2852 on 1 procs for 10000 steps with 550 atoms

Performance: 249924.414 tau/day, 578.529 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 9.637      | 9.637      | 9.637      |   0.0 | 55.75
Bond    | 0.025444   | 0.025444   | 0.025444   |   0.0 |  0.15
Neigh   | 4.6852     | 4.6852     | 4.6852     |   0.0 | 27.11
Comm    | 0.65556    | 0.65556    | 0.65556    |   0.0 |  3.79
Output  | 0.0099883  | 0.0099883  | 0.0099883  |   0.0 |  0.06
Modify  | 2.1895     | 2.1895     | 2.1895     |   0.0 | 12.67
Other   |            | 0.08248    |            |       |  0.48

Nlocal:        550.000 ave         550 max         550 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        2367.00 ave        2367 max        2367 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:        36781.0 ave       36781 max       36781 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 36781
Ave neighs/atom = 66.874545
Ave special neighs/atom = 0.36363636
Neighbor list builds = 840
Dangerous builds = 0
Total wall time: 0:00:17
